Cloudy Skies
by that-fourth-chaos-emerald
Summary: After Metal Sonic's failure, Eggman realizes the only thing strong enough to defeat Sonic is- well, Sonic. After a lot of research and experimentation, he finally creates an almost perfect organic copy of his rival. His creation, known as Experiment #246, is experiencing the real world outside Eggman's fortress for the first time. Will he follow his creator, or join Sonic's fight?
1. The Stranger

A gust of wind blew through the trees in a quiet, green forest.

The leader of The Resistance, Sonic the Hedgehog, was going for a revitalizing run, breathing in the fresh air that surrounded him. He grinned as he ran at a relaxed speed of 250mph.

' _What a beautiful morning_ ,' he thought to himself, looking above him at the birds chirping in the trees. He smiled and began whistling a happy little tune, feeling completely content and stress-free for the first time in a long time.

Eggman had been very quiet for quite a while, and it was rumored that he had given up on his plan to take over the world. However, Sonic kept up his guard. He still prepared the weaponry every morning, continued to train hard every day, and had a 24/7 guard system surrounding their base that was tucked away in the serene forest. If even a rock was thrown into their territory, they would know about it.

As Sonic continued to whistle his carefree tune, a sudden gust of wind blew past him and a streak of white zipped through the forest trees ahead of him.

Sonic's song was cut short as he slowed a bit in shock. "What in the world…?" His carefree demeanor vanished as he picked up his pace, determined to catch whatever it was that was faster than him. He increased his speed to 400mph. The object was just in his sight, but still pulling ahead of him.

"'Guess my leisurely run is over," Sonic muttered to himself as he sped up to 500mph.

Suddenly, the white object turned sharply to the right. Sonic almost didn't react fast enough, and had to skid in order to make the tight turn. Now the object seemed to be going even faster as Sonic increased his speed yet again, now going 600mph. At this point, he could feel his legs starting to get fatigued. The object made another turn, and this time Sonic was ready to react quickly, staying right on its tail.

"What the heck is this thing?!" he asked himself, speeding up yet again to 700mph. He was starting to sweat, his heart-rate rising.

As Sonic sped up, the streak of white sped up as well, seeming to react to Sonic's speed.

Sonic grimaced as he sped up to his maximum speed of 765mph.

For the first time in his life, Sonic shouted: "Hey you! Slow down!"

In that moment, it lost its concentration and crashed into one of the forest trees.

Sonic skidded to a halt, and due to his high speed, he only managed to come to a complete stop quite a few yards away from the object. He raced back to discover what it was that he couldn't catch up with. As he neared the tree he slowed down, sneaking up on the object in case it was dangerous. He peered around the tree carefully, and to his great surprise, a young hedgehog no older than 7 was lying unconscious at the base of the tall tree.

The young hedgehog was mostly white, but upon closer inspection he had subtle streaks of blue within his fur. He had messy, short quills that stuck out in all directions, and a bump was already forming on his forehead from the crash. Sonic cautiously picked up the young hedgehog, cradling him gently in his arms. He took a quick scan of the forest, checking to see if this little guy had company. However, the forest was as quiet as it had been before the boy had blazed through it. Sonic looked down at the boy in his arms, a look of concern on his face. "Don't worry, little buddy, I'll take care of ya," he promised the kid, racing back to base at full speed.

* * *

The young hedgehog's head throbbed as his eyes slowly opened. The room he was in was extremely bright as sunlight filtered through an open window, and he quickly shut them again. He put a hand to his head and felt bandaging covering a large bump on his forehead.

He couldn't remember what happened. The little hedgehog's foggy mind attempted to create a timeline.

' _I was in The Lab,'_ he recalled. _'I was training with The Doctor. I broke free. I was stronger than him. He couldn't stop me. That's when I ran. The Doctor couldn't catch me. I ran to the place full of those Tall Things. The Outside is so big… I ran and ran and ran, then—'_

"Hey there!"

His eyes flew open. He sat up and looked around him frantically. A blue hedgehog was smiling at him, a folded blanket in one hand and a glass of water in the other. The smaller hedgehog sat in stunned silence.

"Don't worry, you're safe," the older hedgehog said with a charming smile, setting the glass on the nightstand. "You hit your head pretty hard, but you're gonna be just fine."

The white hedgehog blinked. ' _I know you…'_ he thought. _'Blue spikes, red shoes, green eyes; It must be—'_

"I'm Sonic," he said, kneeling down beside the bed and smiling at the young boy. "Sonic the Hedgehog. What's your name, kiddo?"

The young hedgehog's face turned from disbelief to complete and utter rage, and suddenly the kid threw himself at Sonic, his fists flying frantically.

"Woah, what the—?!" He caught Sonic in the eye before the blue hedgehog was able to restrain the suddenly violent youngster.

"Agh! Why you little _—_!" Sonic had the little guy in a headlock, pinning him to the ground but not hurting him. His legs flailed wildly, desperately trying to hit Sonic one more time.

"Let go of me, you monster!" he screamed.

"Hey, hey, take a chill pill, will ya?" Sonic said calmly as he easily restrained the small hedgehog. "Tails," Sonic said into his wrist communicator. "I have a little bit of a situation here."

A voice crackled through his communicator. "I'm on my way!"

Sonic yelped as he narrowly avoided getting a bite to his forearm, swiping his arm away. The kid took that opportunity to break free of Sonic's hold. Both hedgehogs quickly stood up from the ground, watching the other very closely.

Sonic put his hands up. "Hey kid, I don't wanna hurt ya, alright?"

The young hedgehog launched himself at Sonic again, screaming violently, and Sonic quickly side-stepped to avoid the clobbering. However, he underestimated the kid's reflexes, and the kid managed to throw a punch to Sonic's gut, knocking the wind out of him.

"Oof!" Sonic doubled over, clutching his stomach. Then, to the kid's surprise, he chuckled a little. "Ya know, for a pipsqueak, you're pretty strong," he choked out with a cocky grin.

"Shut up!" the white hedgehog ordered, sending a powerful kick into Sonic's leg.

Sonic had no time to react, and he fell to the ground, cringing in pain. ' _Where did this kid come from?! And how is he so fast?!'_

The boy stood over Sonic, glowering down at him, and for a brief moment Sonic actually felt quite afraid of this little kid.

"Your tyranny on this world must end!" the kid yelled. "Sonic the Hedgehog must be obliterated; erased from this planet by any means necessary!"

"Wow, did your mommy teach you those words?~" Sonic retorted with a teasing grin.

The kid's expression quickly changed from murderous to confusion, his head tilting to the side slightly in curiosity. "'Mommy?'" he repeated, as if hearing the word for the first time.

Before Sonic could respond, the kid wobbled a little then fell limply to the ground. Tails stood behind him, holding a syringe in his hand.

"Sonic, are you alright?!" Tails immediately kneeled to the ground, checking his brother over for injuries. "Your eye!" he exclaimed, Sonic's eye already turning purple from the punch it received earlier.

"Yeah, yeah, I'm fine," Sonic brushed him off, grimacing a little as he crawled over to the kid lying unconscious a few feet away from him. He had hit him in the stomach surprisingly hard.

"Who is this?" Tails questioned.

"I don't know…" Sonic said, looking into the young hedgehog's face. In his unconscious state, the little guy looked peaceful. Absolutely harmless. "But I'm going to find out."


	2. Snowstorm

_I want to thank you all for your positive reviews! They really mean a lot to me. Please continue to give feedback, I really appreciate constructive criticism. You all are fantastic! I hope you enjoy Chapter 2!_

* * *

Lights on.

Get up.

The 6-year-old hedgehog's eyes shot open and he quickly climbed out of his cot. He started putting on his Favorite-New-Red-and-White Shoes, not wasting a moment. He knew The Doctor would get angry if he wasn't ready fast enough.

Beside his bed was a small chute built into the wall. Three times a day The Doctor sent down something for him to eat. In the morning, it was always a granola bar. Sometimes, if the little hedgehog pleaded enough, The Doctor would send him some peanut butter too. Peanut butter was his absolute favorite thing—besides his Favorite-New-Red-and-White Shoes, of course.

He hopefully reached his hand into the chute and pulled out the usual granola bar, but to his disappointment there was no peanut butter in sight. The little hedgehog frowned and ate the granola bar plain, sulking as he chewed. _Maybe tomorrow The Doctor will give me some_ , he thought hopefully.

After finishing his breakfast, he zipped over to his sink, which was only a few feet from his bed, and started brushing his teeth. _'I don't want to have to fix your cavities, so brush twice a day,'_ he recalled The Doctor saying as he scrubbed away.

The 6-year-old stared long and hard at his quills in the mirror. _Definitely bluer,_ he observed. His white fur was slowly but surely turning a light shade of blue, leaving only a few white streaks of pure white behind in his short, messy quills.

The little hedgehog looked around his room through his mirror's reflection, almost as if to make sure everything was as he left it before he went to sleep. _Sink: check. Bed: check. Dresser: check. Shower: check. Toilet: check._ He looked down at his feet. _Favorite-New-Red-and-White Shoes: check and check._ He grinned broadly. The Doctor had given them to him yesterday. The little hedgehog was so ecstatic when he got the scarlet sneakers he thought he was going to explode! His old shoes were a boring grey color. Plus, they didn't fit him right anymore! Maybe they shrank? The Doctor told him his old shoes fit funny because he had grown, but he didn't feel any bigger.

The white hedgehog had everything he needed in his room, including his bestest friend in the whole wide world: Max.

"Goo' mornin' Max!" he said cheerfully around his toothbrush.

Max the Teddy Bear imaginarily responded with a pleasant 'good morning.'

The kid grinned before spitting into the sink. "Guess what? The Doctor said he has a surprise for me today! What do you think it could be?"

The little stuffed bear sat silently on his bed.

"Yeah, maybe…" the hedgehog responded, pondering his friend's imaginary words. "Do you think it's something from Outside?"

' _Outside is dangerous. You aren't ready to go there yet,'_ The Doctor had told him time and time again.

The hedgehog's head whipped around as he heard a mechanical click. He immediately stood up straight, his hands at his sides as he faced the entrance to his room.

Door opens.

Smile.

"Hello, E246," Doctor Eggman greeted the little hedgehog, stepping inside his small room.

"Good morning, Doctor!" the boy responded cheerfully, grinning widely. _'Always treat me with respect,'_ he recalled The Doctor saying to him.

"I see you're up and ready to train this time," Eggman observed.

E246 nodded. "Yes, 'lights on, get up,'" he quoted his creator.

Eggman nodded with approval. "Very good. You're learning very quickly."

A genuine smile appeared on the boy's face. He always liked it when The Doctor praised him.

"Alright," Eggman said. "Recite our mission statement."

E246 swallowed hard. He sometimes had a hard time remembering his words, and The Doctor didn't like it when he messed up.

"Sonic the Hedgehog is Priority Number One. Sonic the Hedgehog is the enemy of the All-Powerful Genius Doctor Eggman…" he took a moment to remember the next sentence, fidgeting with his hands. "Sonic the Hedgehog must be obliterated. He must be erased from this planet by any means necessary."

"Correct," The Doctor affirmed.

E246 sighed a bit in relief. He didn't like it when The Doctor got angry with him...

"But don't do that thing with your hands. You look like some sort of nutcase."

He immediately dropped his hands back down to his sides, shrinking a little. He didn't _think_ he looked like a case for holding peanuts. Or did he? "Yes, Doctor…" he responded.

"Come now, it's time to run," Doctor Eggman said.

The little hedgehog obediently followed his creator down the hallway towards what he liked to call the Running Room. E246 enjoyed going there most of the time. Sometimes he didn't.

Sometimes his legs hurt, and sometimes he felt weak and icky, but The Doctor still made him run. Always. The young hedgehog didn't feel icky today, though. He was almost bouncing off the walls with anticipation, ready to try running in his Favorite-New-Red-and-White Shoes his creator had given him the day before. He stared at his feet as he walked, admiring how the fluorescent lights reflected off his shiny shoes. His favorite part was the gold buckle securing them to his feet; it shined the brightest in the light. Yes, they were _much_ better than his Boring-Old-Grey Shoes, he decided.

E246 zipped into the Running Room, feeling like he might explode while waiting for Eggman to set up the Running Machine, or as The Doctor called it, a "High Velocity Tracking Something-or-Other." E246 couldn't remember the big words.

As usual, Eggman kneeled down and started sticking monitors all over the little guy's body.  
"What's my surprise?" E246 asked, trying to take his mind off of his excited feet.

"Well, if I told you it wouldn't be a surprise, now would it?" The Doctor responded matter-of-factly.

"Is it from Outside?" he pried, determined to get a hint.

"Why on Mobius would you want something from _outside_?" Eggman asked, saying "outside" as if it were a dirty word.

"I…" he started fidgeting, looking down at his hands. "I don't know…"

His creator sighed, pausing his work for a moment and putting his hands on the little hedgehog's shoulders. "Look at me."

E246 slowly lifted his eyes to meet his gaze.

"What have I told you about outside?" he asked calmly.

"I-It's ugly," he stuttered nervously, "and it's e-evil."

The Doctor smiled and nodded. "That's right." He looked into E246's eyes, his expression now hard as stone. "When you're ready to go outside one day, I want you to destroy everything. _Everything_ is ugly. _Everything_ is evil. Do you understand?"

E246 nodded, and The Doctor smiled.

"Good boy. Now let's start running."

* * *

E246's eyes shot open. Just as before, his head was throbbing, and yet again he was in a place he didn't recognize. This particular place, however, was not quite as pleasant as the last location he had woken up in.

The room he was in was small; much smaller than his own room back at The Doctor's. There were three cinder block walls and a fourth made of vertical metal bars, allowing him to see out into the hallway.

The little hedgehog attempted to sit up in his cot so he could get a better look around, but he soon discovered that each of his limbs were tied down firmly to the bedframe. He struggled against them, attempting to loosen their tight grip.

"Hey, let me go!" he demanded, tugging violently at his restraints. The little hedgehog quickly figured out that the more he yanked at his cuffs the tighter they clenched around his wrists and ankles. When the pain became unbearable, he stopped struggling and collapsed back onto the bed.

"Ya know, for a twerp, you're pretty strong," he heard a gruff voice say.

E246 lifted his head in an attempt to find the source of the voice through the bars. His eyes fell upon a red echidna who was standing calmly on the other side with his arms crossed. "But guess what, kid? I'm stronger, so don't try anything stupid." Knuckles then lifted his wrist to his mouth, speaking into his communicator. "Sonic, our little prisoner is awake."

"Roger that, I'm on my way down," a voice crackled through the speaker.

"You're Knuckles the Echidna," the little hedgehog said unexpectedly.

The red echidna was taken aback, but quickly put his guard back up, his face returning to its stone-like expression. "You knowing my name doesn't change anything, pipsqueak. Sonic put me in charge of guarding your cell until he figures out what to do with you, and I plan to take my assignment very seriously."

"I know more than just your name," E246 responded matter-of-factly. "Knuckles the Echidna. Guardian of the Master Emerald and the lone survivor of his tribe. Age: 16. Height: 110cm. Weight: 88lbs. Favorite food: grapes. Affiliation with Priority One: member of the Resistance. Weaknesses: easily fooled— "

"Hey, I am not!" Knuckles retorted, his cheeks turning almost as red as his fur.

"—and has a bad temper," the little hedgehog finished.

Knuckles' fists were shaking, his whole body tensing in agitation. "Why you little-!"

"What's going on down here?" a much calmer voice asked from down the hall.

"He started it!" Knuckles declared, pointing an accusing finger at the white hedgehog.

Sonic the Hedgehog came into E246's view as he neared the entrance to his cell. The young hedgehog could clearly see a purple splotch covering the older hedgehog's left eye, and he felt a feeling of pride wash over him. _'_ I _did that!_ ' he thought. _'The Doctor would be so proud!'_

"I apologize for my friend Knuckles. He has a bit of a short fuse," Sonic said, with a teasing smirk.

"I do not!" Knuckles yelled, however Sonic ignored his protests.

"By the way, nice shoes," he said, pointing out the hedgehog's red and white sneakers. "They're just like mine," he grinned. "Are you a fan?"

E246 sat in silence, but never broke eye contact with the older hedgehog.

"I never did catch your name, kid," Sonic said, smiling almost toopleasantly towards the white hedgehog. "Will you at least tell me that much?"

E246 responded with a glare.

The older hedgehog sighed with a shrug of his shoulders. "Fine then. I guess I'll have to call you Snowball," he said with an amused smile. "Ya know, cuz of your white fur?"

"I think he gets it, Sonic," Knuckles grumbled, clearly not as amused as Sonic was by the nickname.

The little hedgehog, however, certainly did _not_ get it. He had never heard of a "snowball." He hoped it was something really intimidating and cool.

"You're lucky Tails happened to be working on one of his sleeping dart prototypes," Sonic said, "or else I would have two black eyes." He smiled one of his trademark grins. "So, Snowball, are you gonna tell me why you attacked me?"

E246 cleared his throat. "Sonic the Hedgehog is Priority Number One. Sonic the Hedgehog is the enemy of the All-Powerful Genius Doctor Eggman. Sonic the Hedgehog must be obliterated. He must be erased from this planet by any means necessary," he said as menacingly as he could. ' _I didn't mess up!'_ the kid celebrated internally.

"Alright then," Sonic responded after a brief pause. "You're working with Eggman."

"Yes! The All-Powerful Genius Doctor Eggman; the Ruler of Mobius!" he said proudly. "He's gonna make The Outside better! He told me so himself!" The little hedgehog grinned, awaiting Sonic's reaction. The Doctor was feared by all; there's no way Sonic wouldn't be intimidated now!

"Riiiiight…" Sonic said sarcastically, scratching his ear lazily. "Old Eggbreath's been feeding you a bunch of lies, squirt."

That wasn't quite the reaction E246 had expected. "He does not feed me lies!" he argued. "He feeds me granola bars, sometimes with peanut butter if I ask for it!"

Sonic was caught off guard, having forgotten for a moment that he was interrogating a young child. He burst into laughter, unable to hide his amusement at the odd response.

E246 was confused. What was so funny about granola bars and peanut butter?

"You're not quite the enemy I would have expected Eggman to send to destroy me," Sonic said, still chuckling a little.

The young hedgehog frowned. Why wasn't Sonic scared of him? Shouldn't he be terrified?

"How old are you, kiddo?" Sonic asked with a charming smile.

 _This is all wrong._

The young hedgehog squirmed a little. "Let me go."

"And why should we do that?" Sonic said, putting his hands on his hips.

"I…I uh…" the kid's mind raced, thinking of an excuse. "I need to use the toilet!"

Sonic shrugged. "I guess that's a valid reason." He stepped into E246's cell and looked down at him with a cocky grin. "You're not gonna sock me in the eye again once I let you out of these cuffs, are you?"

The young hedgehog swallowed, hesitating before asking the question that had been gnawing at the back of his mind since he had woken up. "Are you gonna kill me?"

Sonic's grin faltered for a moment, but then he smiled, his emerald eyes genuine. "That's not how we do things here." He then started removing the little hedgehog's restraints, never letting down his guard. He knew this kid was stronger than he looked.

However, E246 didn't take the opportunity to launch another attack against the blue hedgehog and instead calmly followed him down the dim hallway. To his surprise, he felt a gentle hand on his shoulder. He looked up at the older hedgehog, not letting down his guard.

"Just so you know, Snowball, you don't have to be scared of us," Sonic said with a kind smile. "A true Freedom Fighter believes everyone deserves a chance."

E246's gaze returned to the concrete floor below his feet, his mind racing with confusion.

Sonic the Hedgehog wasn't as evil as he expected.


End file.
